Gplas output

README.md

@@ -77,7 +77,7 @@ usage: plaScope.sh [OPTIONS] [ARGUMENTS]
 General options:
   -h, --help		display this message and exit
   -v, --version		display version number and exit
-  -n, --no-banner	don't print beautiful banners
+  -n, --no-banner	do not print beautiful banners
   -t			number of threads[OPTIONAL] [default : 8]
   -o			output directory [OPTIONAL] [default : current directory]
   --sample		Sample name [MANDATORY]
@@ -92,7 +92,7 @@ Mode 1: SPAdes assembly + contig classification
 Mode 2: contig classification of a fasta file (only if you already have your SPAdes or Unicycler assembly!)
   --fasta		SPAdes assembly fasta file [MANDATORY]
   -a                    Specify the assembler used: spades or unicycler. Default=spades.
-
+  -g                    gplas format [OPTIONAL]. Provide results in format compatible with gplas.
 
 Example mode 1:
 plaScope.sh -1 my_reads_1.fastq.gz -2 my_reads_2.fastq.gz -o output_directory  --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample
@@ -104,7 +104,7 @@ plaScope.sh --fasta my_fastafile.fasta -o output_directory --db_dir path/to/DB -
 
 Github:
 https://github.com/GuilhemRoyer/PlaScope
-````
+```
 
 `PlaScope` uses a database (see [this section](#DB)) made of 3 files.
 The argument `--db_dir` is the path to the directory where these 3 files are located.
@@ -179,4 +179,4 @@ centrifuge-build -p 10 --conversion-table seqid_to_taxid.map --taxonomy-tree nod
 
   - Guilhem Royer (CEA-Genoscope, now at Pasteur): design, implementation, evaluation
   - David Valllenet (CEA-Genoscope): design
-  - Julian Paganini (UMC Utrecht): new feature: accept unicycler assemblies
+  - Julian Paganini (UMC Utrecht): new features. 1-Accept unicycler assemblies. 2- Format output for use with gplas

format_results_gplas.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+while getopts :i:o:a:p: flag; do
+	case $flag in
+		i) input_file=$OPTARG;;
+                o) output_file=$OPTARG;;
+                p) plascope_directory=$OPTARG;;
+                a) assembler=$OPTARG
+	esac
+done
+
+
+#1. Create file with proper header to hold the results
+echo -e '"Prob_Chromosome"\t"Prob_Plasmid"\t"Prediction"\t"Contig_name"\t"Contig_length"' > ${output_file}
+#2. Cat the Plascope results and process line by line
+if [[ $assembler == 'unicycler' ]]
+then
+tail -n+2 ${input_file} | while read line
+do
+classification=$(echo $line | cut -f 3 -d ' ')
+contig_number=$(echo $line | cut -f 1 -d ' ')
+echo 'contig_number',${contig_number}
+contig=$(grep -w '>'${contig_number} ${plascope_directory}*fasta | cut -f 2 -d : | sed 's/>//g' )
+length=$(echo $line | cut -f 7 -d ' ')
+if [ $classification == '3' ]
+then
+echo -e 0'\t'1'\t''"Plasmid"''\t''"'$contig'"''\t'$length >> ${output_file}
+elif [ $classification == '2' ]
+then
+echo -e 1'\t'0'\t''"Chromosome"''\t''"'$contig'"''\t'$length >> ${output_file}
+else
+echo -e 0.5'\t'0.5'\t''"Plasmid"''\t''"'$contig'"''\t'$length >> ${output_file}
+fi
+done
+
+else
+tail -n+2 ${input_file} | while read line
+do
+classification=$(echo $line | cut -f 3 -d ' ')
+contig=$(echo $line | cut -f 1 -d ' ')
+length=$(echo $line | cut -f 7 -d ' ')
+if [ $classification == '3' ]
+then
+echo -e 0'\t'1'\t''"Plasmid"''\t''"'$contig'"''\t'$length >> ${output_file}
+elif [ $classification == '2' ]
+then
+echo -e 1'\t'0'\t''"Chromosome"''\t''"'$contig'"''\t'$length >> ${output_file}
+else                                     
+echo -e 0.5'\t'0.5'\t''"Plasmid"''\t''"'$contig'"''\t'$length >> ${output_file}
+fi
+done
+fi

plaScope.sh

@@ -63,7 +63,7 @@ Mode 1: SPAdes assembly + contig classification
 Mode 2: contig classification of a fasta file (only if you already have your SPAdes or Unicycler assembly!)
   --fasta		SPAdes or Unicycler assembly fasta file [MANDATORY]
   -a			Specify the assembler used: spades or unicycler. Default=spades.
-
+  -g			Don't produce the gplas formatted output [OPTIONAL]. 
 
 Example mode 1:
 plaScope.sh -1 my_reads_1.fastq.gz -2 my_reads_2.fastq.gz -o output_directory  --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample
@@ -206,7 +206,7 @@ local contigcov=${CONTIGCOV}
 local contiglength=${CONTIGLENGTH}
 local hitlength=${HITLENGTH}
 
-awk -F'\t' -v contigcov=${contigcov} -v contiglength=${contiglength} -v hitlength=${hitlength} '
+awk -F'\t' -v contiglength=${contiglength} -v hitlength=${hitlength} '
 BEGIN {
 TPLASCOPERES[0]="unclassified"
 TPLASCOPERES[1]="unclassified"
@@ -218,12 +218,8 @@ OFS="\t"
 getline
 }
 
-{clab=$1; split(clab,T,":") ; ccov=T[5];
-
-if ( $7>=contiglength && $6>=hitlength && ccov>contigcov )  print $1,TPLASCOPERES[$3]
-
+{ if ( $7>=contiglength && $6>=hitlength )  print $1,TPLASCOPERES[$3]
 else print $1,TPLASCOPERES[0]
-
 }' $plascopeextendres
 
 }
@@ -271,7 +267,7 @@ local contigfile="$1"
 local contigsortingfile="$2"
 local contigfileprefix="$3"
 
-awk -F'\t' -v contigfileprefix=${contigfileprefix} '
+awk -F'\t| ' -v contigfileprefix=${contigfileprefix} '
 NR==FNR{Tcontig[">"$1]=$2;next}
 
 /^>/ {
@@ -296,7 +292,7 @@ output { print >  output }' $contigsortingfile $contigfile
 #Establish default value for assembler
 assembler='spades'
 
-while getopts ":1:2:o:t:-:h:v:n:a:" optchar; do
+while getopts ":1:2:o:t:-:h:v:n:a:g" optchar; do
 	case "${optchar}" in
 		 -)
 			case "${OPTARG}" in
@@ -349,6 +345,10 @@ while getopts ":1:2:o:t:-:h:v:n:a:" optchar; do
 		a)
 			assembler=${OPTARG}
 			;;
+                g)
+                        gplas_output='true'
+                        ;; 
+
 		?)
 			usage
 			exit 1
@@ -509,6 +509,11 @@ fi
 
 contig_extraction ${FASTA} ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_list ${OUTPUT}/${PREFIX}_PlaScope/PlaScope_predictions/${PREFIX}
 
+#Create gplas formatted result file
+if [ -z "${gplas_output+x}" ]; then
+   mkdir ${OUTPUT}/gplas_formatted_results
+   ./format_results_gplas.sh -i ${OUTPUT}/${PREFIX}_PlaScope/Centrifuge_results/${PREFIX}_extendedresult -o ${OUTPUT}/gplas_formatted_results/${PREFIX}_plasmid_prediction.tab -p ${OUTPUT}/${PREFIX}_PlaScope/PlaScope_predictions/ -a ${assembler}
+fi
 echo "If you use PlaScope please cite: ..."
 
 exit 0